Sample Resequencing Stats

Note: The mutation counts shown below represent unfiltered mutation sets.

ALE, Flask, Isolate	Predicted Mutations	Mean Coverage	Total Reads	Percent Mapped	Mapped Reads	Average Read Length
A29 F18 I1 R1	19	60.0	2279412	90.4%	2060588	142.2

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	4,184,543	C→A	P1100Q (CCG→CAG)	rpoB →	RNA polymerase subunit beta

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	4,184,543	0	C	A	97.4%	114.6 / NA	39	P1100Q (CCG→CAG)	rpoB	RNA polymerase subunit beta
Reads supporting (aligned to +/- strand): ref base C (0/0); major base A (14/24); minor base G (1/0); total (15/24)
Fisher's exact test for biased strand distribution p-value = 3.85e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

CTGGCGGTTAAACGCCGTATCCAGCCTGGTGACAAGATGGCAGGTCGTCACGGTAACAAGGGTGTAATTTCTAAGATCAACCCGATCGAAGAT‑ATGCCTTACGATGAAAACGGTACGCCGGTAGACATCGTACTGAACCCGCTGGGCGTACCGTCTCGTATGAACATCGGTCAGATCCTCGAAACCCACCTGGGTATGGCTGCGAAAGGTATCGGCGACAAGATCAACGCCATGCTGAAACAGCAGCAAGAAGTCGCGAAACTGCGCGAATTCA  >  NC_000913/4184404‑4184677

cTGGCGGTTAATCGCCGTATCCAGCCTGGTAACAAGAGGGCAGGGCGTCACGGTAACAAGGGTGTAATTTCTAAGATCAACCCGATCGAAGAT‑ATGCCTTACGATGAAAACGGTACGCCGGTAGACATCGTACTGAACCAGCt                                                                                                                                     <  2:314574/143‑1 (MQ=255)

 tGGCGGTTAAACGCCGTATCCAGCCTGGTGACAAGATGGCAGGTCGTCACGGTAACAAGGGTGTAATTTCTAAGATCAACCCGATCGAAGAT‑ATGCCTTACGATGAAAACGGTACGCCGGTAGACATCGTACTGAACCAGCTg                                                                                                                                    <  1:395910/143‑1 (MQ=255)

 tGGCGGTTAAACGCCGTATCCAGCCTGGTGACAAGATGGCAGGTCGTCACGGTAACAAGGGTGTAATTTCTAAGATCAACCCGATCGAAGAT‑ATGCCTTACGATGAAAACGGTACGCCGGTAGACATCGTACTGAACCAGCTg                                                                                                                                    <  1:546392/143‑1 (MQ=255)

   gCGGTTAAACGCCGTATCCAGCCTGGTGACAAGATGGCAGGTCGTCACGGTAACAAGGTAGGAATTACTAAGATCAACCCGATCGAAGAT‑ATGCCTTACGATGAAAACGGTACGCCGGTAGACATCGTACTGAACCGGCTggg                                                                                                                                  >  1:290026/1‑143 (MQ=255)

       ttACACGCCGTATCCAGCCTGGTGACAAGAGGGCAGGTCGTCACGGTAACGAGGGTGTAATTTCTAAGATCAACCCGATCGAAGAT‑ATGCCTTACGATGAAAACGGTACGCCGGTAGACATCGTACTGAACCAGCTGGGCGTa                                                                                                                              <  2:790909/143‑1 (MQ=255)

        tAAACGCCGTGTCCAGCCTGGTGACAAGATGGCAGGTCGTCACGGTAACAAGGGTGTAATTTCTAAGATCAGCCCGATCTAGGAT‑ATGCCTTACGATGAAAACGGTACGCCGGTAGACATCGTACTGAACCAGCTGGGCGTAc                                                                                                                             <  2:1005559/143‑1 (MQ=255)

            cGCCGTATCCAGCCTGGTGACAAGATGGCAGGTCGTCACGGTAACAAGGGTGTAATTTCTAAGATCAACCCGATCGAAGAT‑ATGCCTTACGATGAAAACGGTACGCCGGTAGACATCGTACTGAACCAGCTGGGCGTACCGtc                                                                                                                         >  1:732594/1‑143 (MQ=255)

               cGTATCCAGCCTGGTGACAAGATGGCAGGTCGTCACGGTAACAAGAGTGTAATTTCTAAGATCAACCCCATCGACGAT‑ATGCCTTACGATGAAAACAGTACACCGGTAGACATCGTACTGAACCAGCTGCGCGTACAGTCACg                                                                                                                      >  2:170607/1‑143 (MQ=255)

                ggaTCCAGCCTGGTGACAAGATGGCAGGTCGTCACGGTAACAAGGGTGTAATTTCTAAGATCAACCCGATCGAAGAT‑ATGCCTTACGATGAAAGCGGTACGCCGGTAGACATCGTACTGAACCAGCTGGGCGTACCGTCTCGt                                                                                                                     <  2:918324/141‑1 (MQ=255)

                 tATCCAGCCTGGTGACAAGATGGCAGGTCGTCACGGTAACAAGGGTGTAATTTCTAAGATCAACCCGATCGAAGAT‑ATGCCTTACGATGAAAACGGTACGCCGGTAGACATCGTACTGAACCAGCTGGGCGTACCGTCTCGTa                                                                                                                    >  1:793444/1‑143 (MQ=255)

                  aTCCAGCCTGGTGACAAGATGGCAGGTCGTCACGGTAACAAGGGTGTAATTTCTAAGATCAACCCGATCGAAGAT‑ATGCCTTACGATGAAAACGGTACGCCGGTAGACATCGTACTGAACCAGCTGGGCGTACCGTCTCGTAt                                                                                                                   >  1:373156/1‑143 (MQ=255)

                     cAGCCTGGTGACAAGATGGCAGGTCGTCACGGTAACAAGGGTGTAATTTCTAAGATCAACCCGATCGACGAT‑ATGCCTTACGATGAAAACGGTACGCCGGCAGACATCGTACTGCACCAGCAGGCCGCACCGCCTCgcccgaa                                                                                                                >  2:189897/1‑137 (MQ=255)

                      aggcTGGGGCCAAGATGGCAGGTCGTCACGGTAACAAGGGTGTAATTTCTAAGATCAACCCGATCGAAGAT‑ATGCCTTACGATGAGAACGGTACGCCGGTAGACATCGTACTGAACCAGCTGGGCGTACCGTCTCGTATGAAc                                                                                                               <  1:592855/140‑1 (MQ=255)

                                     tGGCAGGTCGTCACGGTAACAAGGGTGTAATTTCTAAGATCAACCCGATAGAAGAT‑ATGCCTTACGATGAAAACGATACGCCGGTAGACATCGTACTGAACCAGCTGGGCGTACCGTCTCGTATGAACATCGGTCAGATCCTc                                                                                                <  1:99238/143‑1 (MQ=255)

                                         aGGTCGTCACGGTAACAAGGGTGTAATTTCTAAGATCAACCCGATCGACAATGATG‑CGTACGCTGCACACCGGCCTCCGGTAGACATCGTACTGAACCAGCTGGGCGTACCGTCTCGTATGAACATCGGTCAGATCCTCGaaa                                                                                            <  2:805931/143‑1 (MQ=255)

                                         aGGTCGTCACGGTAACAAGGGTGTAATTTCTAAGATCAACCCGATCGAAGAT‑ATGCCTTACGATGAAAACGGTACGCCGGTAGACATCGTACTGAACCAGCTGGGCGTACCGTCTCGTATGAACATCGGTCAGATCCTCGaaa                                                                                            <  2:599773/143‑1 (MQ=255)

                                                  cGGTAACAAGGGTGTAATTTCTAAGATCAACCCGATCGAAGAT‑ATGCCTTACGATGAAAACGGTACGCCGGTAGACATCGTACTGAACCAGCTGGGCGTACCGTCTCGTATGAACATCGGTCAGATCCTCGAAACCCACCTgg                                                                                   <  1:578915/143‑1 (MQ=255)

                                                  cGGTAACAAGGGTGTAATTTCTAAGATCAACCCGATCGAAGAT‑ATGCCTTACGATGAAAACGGTACGCCGGTAGACATCGTACTGAACCAGCTGGGCGTACCGTCTCGTATGAACATCGGTCAGATCCTCGAAACCCACCTgg                                                                                   <  1:659529/143‑1 (MQ=255)

                                                  cGGTAACAAGGGTGTAATTTCTAAGATCAACCCGATCGAAGAT‑ATGCCTTACGATGAAAACGGTACGCCGGTAGACATCGTACTGAACCAGCTGGGCGTACCGTCTCGTATGAACATCGGTCAGATCCTCGAAACCCACCTgg                                                                                   <  1:100126/143‑1 (MQ=255)

                                                   ggTAACAAGGGTGTAATTTCTAAGATCAACCCGATCGAAGAT‑ATGCCTTACGATGAAAACGGTACGCCGGTAGACATCGTACTGAACCAGCTGGGCGTACCGTCTCGTATGAACATCGGTCAGATCCTCGAAACCCACCTggg                                                                                  <  1:193670/143‑1 (MQ=255)

                                                          aggaggtAATTTCTAAGATCAACGCGATCGAAGAT‑ATGCCTTACGATGAAAACGGTACGCCGGTAGACATCGTACTGAACCAGCTGGGCGTACCGTCTCGTATGAACATCGGTCAGATCCTCGAAACCCACCTGGGTATGGCt                                                                           <  2:701185/138‑1 (MQ=255)

                                                           gggTGTAATTTCTAAGATCAACCCGATCGAAGAT‑ATGCCTTACGATGAAAACGGTACGCCGGTAGACATCGTACTGAACCAGCTGGGCGTACCGTCTCGTATGAACATCGGTCAGATCCTCGAAACCCACATGGGTATGGCTg                                                                          >  2:663224/1‑143 (MQ=255)

                                                            ggTGTAATTTCTAAGATCAACCCGATCGAAGAT‑ATGCCTTACGATGAAAACGGTACGCCGGTAGACATCGTACTGAACCAGCTGGGCGTACCGTCTCGTATGAACATCGGTCAGATCCTCGAAACCCCCCTGGGTACGGCTGc                                                                         >  2:912011/1‑143 (MQ=255)

                                                              tgtAATTTCTAAGATCAACCCGATCGAAGAT‑ATGCCTTACGATGAAAACGGTACGCCGGTAGACATCGTACTGAACCAGCTGGGCGTACCGTCTCGTATGAACATCGGTCAGATCCTCGAAACCCACCTGAGCATGGCAGCGa                                                                       >  2:1065935/1‑143 (MQ=255)

                                                                tAATTTCTAAGATCATCCCGATCGAAGAT‑ATGCCTTACGATGAAAACGGTACGCCGGTAGACATCGTACTGAACCAGCTGGGCGTACCGTCTCGTATGAACATCGGTCAGATCCTCGAAACCCACCTGGGTATGGCTGCGaaa                                                                     <  1:992252/143‑1 (MQ=255)

                                                                       tAAGATCAACCCGATCGAAGCT‑ATGCCTTACGATGAAAACGGTAAGCCGGTAGACATCGTACTGACCCAGCTGGGCGTACCGTCTCGTCTGAACATCGGTCAGATCCTCGAAACCCACCTGGGTATGGCTGCGTAAGGTCTCg                                                              >  1:648505/1‑143 (MQ=255)

                                                                           aTCAACCCGATCGAAGAT‑ATGCCTTACGATGAAAACGGTACGCCGGTAGACATCGTACTGAACCAGCTGGGCGTACCGTCTCGTATGAACATCGGTCAGATCCTCGAAACCCACCTGGGTATGGCTGCGAAAGGTATCGGCGa                                                          <  1:820012/143‑1 (MQ=255)

                                                                                     tCGCAGAT‑TTGCCTTACGATGAAAACGGTACGCTGGTTGTCATCGTACTGAATCAGCTGGGCGTACCGCCTCGTAGGAACATCGGTCAGATCCCCGCGAGACACTTGGGTTTGGCTGCGAAAGGTATCGGCGACAAGATCAAc                                                <  1:586306/143‑1 (MQ=255)

                                                                                       gAAGAT‑ATGCCTTACGATGAAAACGGTACGCCGGTAGACATCGTACTGAACCAGCTGGGCGTACCGTCTCGTATGAACATCGGTCAGATCCACGAAACCCACCTGGGTATGGCTGCGAAAGGTATCGGCGACAAGAGCAACGc                                              >  2:655762/1‑143 (MQ=255)

                                                                                        aaGAT‑ATGCCTTACGATGAAAACGGTACGCCGGTAGACATCGTACTGAACCAGCTGGGCGTACCGTCTCGTCTGAACATCGGTCAGATCCTCGAAACCCACCTGGGTATGGCCGCGAAAGGTATCGGCGACCAGAACAACGcc                                             >  2:1119472/1‑143 (MQ=255)

                                                                                        aaGAT‑ATGCCTTACGATGAAAACGGTACGCCGGTAGACATCGTACTGAACCAGCTGGGCGTACCGTCTCGTATGAACATCGGTCAGATCCTCGAAACCCACCTGGGTATGGCTGCGAAAGGTATCGGCGACAAGATCAACGcc                                             >  2:823285/1‑143 (MQ=255)

                                                                                              atGCCTTACGATGAAAACGGTACGCCGGTAGACATCGTACTGAACCAGCTGGGCGTACCGTCTCGTATGAACATCGGTCAGATCCTCGAAACCCACCTGGGTATGGCTGCGAAAGGTATCGGCGACAAGATCAACGCCATGCt                                        <  2:776323/143‑1 (MQ=255)

                                                                                                      cgctGAAAACGGTCCGCCGGTAGACATCGTACTGAACGAGCTGGGCGTACCGTCGCGTATGAACATCGGTCAGATCCGCGAAACCCACCTGGGTATGGCTGCGAAAGGTATCGGCGACAAGATCAACGCCATGCTGAAAcagc                                <  1:785966/140‑1 (MQ=255)

                                                                                                      cGATGAAAACGGTACGCCGGTAGACATCGTACTGAACCAGCTGGGCGTACCGTCTCGTATGAACATCGGTCAGATCCTCGAAACCCACCTGGGTATGGCTGCGAAAGGTATCGGCGACAAGATCAACGCCATGCTGAAAcagc                                <  2:191107/143‑1 (MQ=255)

                                                                                                           caaaCGGCACGCCGGTAGACATCGTACTGACCCAGCTGGGCGTACCGTCTCGTATGAACATCGGTCAGATCCTCAAAACCCACCTGGGTATGTCTGCGAAAGGTATCGGCGACAAGATCAACGCCATGCTGAAACAGCAGCaa                           <  1:342023/142‑1 (MQ=255)

                                                                                                           aaaaCGGTACGCCGGTAGACATCGTACTGAACCAGCTGGGCGTACCGTCTCGTATGAACATCGGTCAGATCCTCGAAACCCACCTGGGTATGGCTGCGAAAGGTATCGGCGACAAGATCAACGCCATGCTGAAACAGCAGCaa                           <  1:877338/143‑1 (MQ=255)

                                                                                                                           aGACATCGTACTGAACCAGCTGGGCGTACCGTCTCGTATGAACATCGGTCAGATCCTCGAAACCCACCTGGGTATGGCTGCGAAAGGTATCGGCGACAAGATCAACGCCATGCTGACACAGCAGCAAGAAGTCGCGAACCTgc           >  2:884953/1‑143 (MQ=255)

                                                                                                                               aTCGTACTGAACCAGCTGGGCGTACCGTCTCGTATGAACATCGGTCAGATCCTCGAAACCCACCTGGGTATGGCTGCGAAAGGTATCGGCGACAAGATCAACGCCATGCTGAAACAGCAGCAAGAAGTCGCGAAACTGCGCGa       >  1:847701/1‑143 (MQ=255)

                                                                                                                                    aCTGAACCAGCTGGGGGTACCGTCTCGTATGAACATCGGTCAGATCCTCGAAACCCACCTGGGTATGGCTGCGAAAGGTATCGGCGACAAGATCAACGCCATGCTGAAACAGCAGCAAGAAGTCGCGAAACTGCGCGAATTCa  <  2:467399/143‑1 (MQ=255)

CTGGCGGTTAAACGCCGTATCCAGCCTGGTGACAAGATGGCAGGTCGTCACGGTAACAAGGGTGTAATTTCTAAGATCAACCCGATCGAAGAT‑ATGCCTTACGATGAAAACGGTACGCCGGTAGACATCGTACTGAACCCGCTGGGCGTACCGTCTCGTATGAACATCGGTCAGATCCTCGAAACCCACCTGGGTATGGCTGCGAAAGGTATCGGCGACAAGATCAACGCCATGCTGAAACAGCAGCAAGAAGTCGCGAAACTGCGCGAATTCA  >  NC_000913/4184404‑4184677

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 8 ≤` `ATCG/ATCG` `< 12 ≤` `ATCG/ATCG` `< 27 ≤` `ATCG/ATCG` `< 41 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A